• algorithm
  • He has led the effort creating various NGS analysis pipelines, as well as developing FusionMap , a widely used fusion gene detection algorithm to detect fusion genes at both transcript and genomic levels. (omicsoft.com)
  • As a result, a network motif detection algorithm would pass over more candidate sub-graphs if we insist on frequency concepts F2 and F3. (wikipedia.org)
  • One other limitation to Gene Set Enrichment Analysis is that the results are very dependent on the algorithm that clusters the genes, and the number of clusters being tested. (wikipedia.org)
  • For instance it can be done by the application of a correlation-based inference algorithm, as will be discussed below, an approach which is having increased success as the size of the available microarray sets keeps increasing Signal transduction networks (very important in the biology of cancer). (wikipedia.org)
  • microarrays
  • In order to seek out genes associated with diseases, researchers utilized DNA microarrays, which measure the amount of gene expression in different cells. (wikipedia.org)
  • Researchers would perform these microarrays on thousands of different genes, and compare the results of two different cell categories, e.g. normal cells versus cancerous cells. (wikipedia.org)
  • In GSEA, DNA microarrays, or now RNA-Seq, are still performed and compared between two cell categories, but instead of focusing on individual genes in a long list, L, the focus is put on a gene set. (wikipedia.org)
  • promoter
  • A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas Melloul et al. (wikipedia.org)
  • For example, it identified the bacteriorhodopsin regulon, assigned additional genes to this regulon with apparently unrelated function, and detected its known promoter motif. (biomedcentral.com)
  • The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which increased the rate of transcription from a linked promoter. (wikipedia.org)
  • Thus gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). (wikipedia.org)
  • By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. (wikipedia.org)
  • Although it is not yet clearly understood, it is thought that the reverse transcript guides methylation complexes and/or histone-modifying complexes to the promoter regions of the sense transcript and cause an inhibition of expression from the gene. (wikipedia.org)
  • During the process of transcription of cis-NATs, the transcriptional complexes assemble in the promoter regions of the gene. (wikipedia.org)
  • analyze
  • The dynamics of this network is difficult to analyze, notably due to a lack of quantitative information on parameter values. (springer.com)
  • The recent availability of whole-genome scale data sets that investigate complementary and diverse aspects of transcriptional regulation has spawned an increased need for new and effective computational approaches to analyze and integrate these large scale assays. (nih.gov)
  • Researchers analyze whether the majority of genes in the set fall in the extremes of this list: the top and bottom of the list correspond to the largest differences in expression between the two cell types. (wikipedia.org)
  • This allows the researcher to analyze regulatory data using their own conditions as to the suitability of the supporting evidence. (wikipedia.org)
  • experimental
  • A classic approach to experimental perturbation is to knock out a specific gene by a targeted mutation and see what happens. (macdevcenter.com)
  • Be cause genes may be co-regulated only across a subset of all observed experimental conditions, biclustering (clustering of genes and conditions) is more appropriate than standard clustering. (biomedcentral.com)
  • However, gene transcript levels can be correlated either by chance (due to experimental noise or systematic error) or because of indirect effects, and therefore they might not actually be directly co-regulated. (biomedcentral.com)
  • Stormo's research combines experimental and computational approaches to understand regulation of gene expression. (wikipedia.org)
  • Metabolism
  • The influence of metabolites on enzyme gene regulation is a necessary arrangement to make the systems (both metabolic and regulatory) responsive to environmental changes and maintain the homeostasis of metabolism. (biomedcentral.com)
  • These include intriguing instances of differing motif dosages and differing combinatorial motif control that promote regulatory specificity in rRNA metabolism under differing physiological processes. (nih.gov)
  • genomic
  • The Centre for Genomic Regulation (CRG, Centre de Regulació Genòmica in Catalan) is a biomedical and genomics research centre based on Barcelona. (wikipedia.org)
  • Another research line involves identification and characterization of genomic regions associated with gene regulation. (wikipedia.org)
  • Current evidence has suggested a variety of regulatory roles for NATs, such as RNA interference (RNAi), alternative splicing, genomic imprinting, and X-chromosome inactivation. (wikipedia.org)
  • functional
  • A significant correlation was, however, observed for H19, COL2A1, and miR-675 expression levels in OA tissue, and functional regulation of these candidate molecules was assessed under anabolic and catabolic conditions. (ebscohost.com)
  • Cis-regulatory modules are one of several types of functional regulatory elements. (wikipedia.org)
  • There are two types of transcription factor inputs: those that determine when the target gene is to be expressed and those that serve as functional drivers, which come into play only during specific situations during development. (wikipedia.org)
  • For the most part, even with the presence of functional overlap between cis-regulatory modules of a gene, the modules' inputs and outputs tend to not be the same. (wikipedia.org)
  • reconstruct
  • To enable such modeling Carnegie Mellon University researchers have developed a method that learns a probabilistic model which integrates expression similarity with regulatory information to reconstruct the dynamic developmental cell trajectories. (rna-seqblog.com)
  • In a PLoS Biology paper, institute founding director Eric Schadt led a research team that utilized six different types of data (metabolite concentration, gene expression, DNA variation, DNA-protein binding, protein-metabolite interaction, and protein-protein interaction) to reconstruct networks involved in cell regulation. (wikipedia.org)
  • molecules
  • In order to identify molecules representing putative key regulators for diagnosis and therapeutic intervention, we analyzed gene expression and microRNA (miR) levels in OA and normal knee cartilage using a customized cartilage cDNA array and quantitative RT-PCR. (ebscohost.com)
  • Approaches
  • Such approaches have led to the determination of the topology of metabolic networks for a great number of organisms [ 4 , 5 ]. (mdpi.com)
  • We adopt two alternative approaches to build those links: inferring the links between metabolites and transcription factors to fit the data or explicitly encoding the general hypotheses of feedback control as links between metabolites and enzyme expressions. (biomedcentral.com)
  • The method uses statistical approaches to identify significantly enriched or depleted groups of genes. (wikipedia.org)
  • Least-angle regression, by Bayesian network or based on Information theory approaches. (wikipedia.org)
  • functionally
  • Co-regulated genes are also often functionally (physically, spatially, genetically, and/or evolutionarily) associated, and such a priori known or pre-computed associations can provide support for appropriately grouping genes. (biomedcentral.com)
  • computational
  • Gary Ge obtained a B.S. in life sciences from Fudan University, M.S. in Statistics and Ph.D. in Computational Biology and Bioinformatics from University of Southern California. (omicsoft.com)
  • Research in computational epigenetics comprises the development and application of bioinformatics methods for solving epigenetic questions, as well as computational data analysis and theoretical modeling in the context of epigenetics. (wikipedia.org)
  • Teichmann's research investigates gene expression and protein complex assembly using both wet laboratory and computational biology techniques. (wikipedia.org)
  • EcoCyc is also a description of the genome and cellular networks of E. coli that supports scientists to carry out computational analyses. (wikipedia.org)
  • Boolean
  • Methods of robustness analysis for Boolean models of gene control networks. (springer.com)
  • In general, gene-regulation functions do not use Boolean logic, although in some cases the approximation of the Boolean logic is still very useful. (wikipedia.org)
  • Within the assumption of the Boolean logic, principles guiding the operation of these modules includes the design of the module which determines the regulatory function. (wikipedia.org)
  • While the assumption of Boolean logic is important for systems biology, detailed studies show that in general the logic of gene regulation is not Boolean. (wikipedia.org)
  • The modelling can be done by a Boolean network, by Ordinary differential equations or Linear regression models, e.g. (wikipedia.org)
  • Microarray Data
  • The Z scores from the application of gene set analysis with gene sets of transcription factor binding sites (TFBSs) were successfully used to represent the activity of TFBSs in a given microarray data set. (biomedcentral.com)
  • The method's founders claim that it is a better way to find associations between MSigDB gene sets and microarray data. (wikipedia.org)
  • regulators
  • The inferred models allow us to 1) identify the feedback links between metabolites and regulators and their functions, 2) identify the active paths responsible for relaying perturbation effects, 3) computationally test the general hypotheses pertaining to the feedback control of enzyme expressions, 4) evaluate the advantage of an integrated model over separate systems. (biomedcentral.com)
  • In the last years, however, an additional class of gene regulators emerged: the microRNAs (miRNAs). (biomedcentral.com)
  • Diseases
  • Control of gene expression is crucial for normal development and maintenance of healthy cells, and alterations from standard coordination programs can lead to severe diseases including cancer. (biomedcentral.com)
  • identification
  • The integration of additional biologically-relevant evidence into a clustering procedure may be used to provide constraints on the identification of groups of co-regulated genes. (biomedcentral.com)